Most of the ballot votes would have been cast in those two weeks, when it was advertised through official channels, gaming news sites, and fan communities like this one. Similar to how the bulk of a YouTube video's views come from its first week or two. I doubt the results changed drastically between the first two weeks to the very end of the ballot, so I don't think that choosing the character two weeks after the ballot started meant anything was "cheated." It was simply working ahead, rather than waiting until the very end and then starting work. Which makes sense, given that Smash Wii U sold very poorly compared to previous entries, hence why Ultimate was conceived that year.
The ballot started like 6-7 months after Bayonetta 2 came out. There was a lot of support for her during that time, including from major YouTubers like Maximillian. Even if the game didn't sell spectacularly, because it was on the Wii U, of course, there was still a strong support base for her during that period, especially among the hardcore gamers who were active at the time.
I don't think Sakurai was lying at all when he stated Bayonetta's performance on the ballot. She was a unique, popular, and Nintendo-exclusive character that came at the right time with the right amount of support. It's easy to question it in retrospect now that much of the Smash community has turned against her due to her dominance in the metagame, but back then, it was a very different atmosphere.
Cloud also did really well on the ballot according to Sakurai, getting more votes than any other FF character, and he's been requested since basically the beginning of time, so adding him made sense, ballot or no.